Check the over-representation of functional terms
Wei Sun
2024-07-09
R libraries.
Read in DE results
## [1] 25835 145## gene_ID PrS_nor_POU2F3_CE_baseMean PrS_nor_POU2F3_CE_log2FoldChange
## 1 ENSG00000000003 1150 -0.0175
## 2 ENSG00000000419 1210 -0.3820
## PrS_nor_POU2F3_CE_lfcSE PrS_nor_POU2F3_CE_stat
## 1 0.0683 -0.256
## 2 0.1210 -3.160## [1] "PrS_nor_POU2F3_CE_padj" "PrS_nor_POU2F3_KO_padj"
## [3] "PrS_nor_POU2F3_PTC_padj" "PrS_nor_PPARG_CE_padj"
## [5] "PrS_nor_PPARG_KO_padj" "PrS_nor_PPARG_PTC_padj"
## [7] "PrS_nor_GCM1_CE_padj" "PrS_nor_GCM1_KO_padj"
## [9] "PrS_nor_GCM1_PTC_padj" "PrS_nor_FOSB_CE_padj"
## [11] "PrS_nor_FOSB_KO_padj" "PrS_nor_FOSB_PTC_padj"
## [13] "PrS_nor_EPAS1_CE_padj" "PrS_nor_EPAS1_KO_padj"
## [15] "PrS_nor_EPAS1_PTC_padj" "PrS_nor_GRHL1_CE_padj"
## [17] "PrS_nor_GRHL1_KO_padj" "PrS_nor_GRHL1_PTC_padj"
## [19] "PrS_hyp_EPAS1_CE_padj" "PrS_hyp_EPAS1_KO_padj"
## [21] "PrS_hyp_EPAS1_PTC_padj" "ExM_nor_ISL1_CE_padj"
## [23] "ExM_nor_ISL1_KO_padj" "ExM_nor_ISL1_PTC_padj"gene_sets = list()
for(it1 in items){
id1 = gsub("_padj", "", it1)
res_k = res[,c(1, grep(id1, names(res)))]
names(res_k) = gsub(paste0(id1, "_"), "", names(res_k))
w_up = which(res_k$log2FoldChange > log2(1.5) & res_k$padj < 0.01)
w_down = which(res_k$log2FoldChange < -log2(1.5) & res_k$padj < 0.01)
gene_sets[[paste0(id1, "_up")]] = res_k$gene_ID[w_up]
gene_sets[[paste0(id1, "_down")]] = res_k$gene_ID[w_down]
}
sapply(gene_sets, length)## PrS_nor_POU2F3_CE_up PrS_nor_POU2F3_CE_down PrS_nor_POU2F3_KO_up
## 299 113 17
## PrS_nor_POU2F3_KO_down PrS_nor_POU2F3_PTC_up PrS_nor_POU2F3_PTC_down
## 6 1 1
## PrS_nor_PPARG_CE_up PrS_nor_PPARG_CE_down PrS_nor_PPARG_KO_up
## 1672 1976 981
## PrS_nor_PPARG_KO_down PrS_nor_PPARG_PTC_up PrS_nor_PPARG_PTC_down
## 1319 1314 1980
## PrS_nor_GCM1_CE_up PrS_nor_GCM1_CE_down PrS_nor_GCM1_KO_up
## 1907 2639 1494
## PrS_nor_GCM1_KO_down PrS_nor_GCM1_PTC_up PrS_nor_GCM1_PTC_down
## 2276 1339 2233
## PrS_nor_FOSB_CE_up PrS_nor_FOSB_CE_down PrS_nor_FOSB_KO_up
## 37 13 167
## PrS_nor_FOSB_KO_down PrS_nor_FOSB_PTC_up PrS_nor_FOSB_PTC_down
## 12 344 150
## PrS_nor_EPAS1_CE_up PrS_nor_EPAS1_CE_down PrS_nor_EPAS1_KO_up
## 480 353 8
## PrS_nor_EPAS1_KO_down PrS_nor_EPAS1_PTC_up PrS_nor_EPAS1_PTC_down
## 11 56 69
## PrS_nor_GRHL1_CE_up PrS_nor_GRHL1_CE_down PrS_nor_GRHL1_KO_up
## 776 1480 642
## PrS_nor_GRHL1_KO_down PrS_nor_GRHL1_PTC_up PrS_nor_GRHL1_PTC_down
## 986 1769 2251
## PrS_hyp_EPAS1_CE_up PrS_hyp_EPAS1_CE_down PrS_hyp_EPAS1_KO_up
## 1625 1191 957
## PrS_hyp_EPAS1_KO_down PrS_hyp_EPAS1_PTC_up PrS_hyp_EPAS1_PTC_down
## 541 1070 608
## ExM_nor_ISL1_CE_up ExM_nor_ISL1_CE_down ExM_nor_ISL1_KO_up
## 1023 466 918
## ExM_nor_ISL1_KO_down ExM_nor_ISL1_PTC_up ExM_nor_ISL1_PTC_down
## 487 696 349Read in gene annotation
## [1] 62700 8## geneId chr strand start end ensembl_gene_id
## 1 ENSG00000000003.16 chrX - 100627108 100637104 ENSG00000000003
## 2 ENSG00000000005.6 chrX + 100584936 100599885 ENSG00000000005
## hgnc_symbol description
## 1 TSPAN6 tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]
## 2 TNMD tenomodulin [Source:HGNC Symbol;Acc:HGNC:17757]##
## FALSE TRUE
## 7 25828## [1] 25828 8## geneId chr strand start end ensembl_gene_id
## 1 ENSG00000000003.16 chrX - 100627108 100637104 ENSG00000000003
## 3 ENSG00000000419.14 chr20 - 50934867 50959140 ENSG00000000419
## hgnc_symbol
## 1 TSPAN6
## 3 DPM1
## description
## 1 tetraspanin 6 [Source:HGNC Symbol;Acc:HGNC:11858]
## 3 dolichyl-phosphate mannosyltransferase subunit 1, catalytic [Source:HGNC Symbol;Acc:HGNC:3005]## t_symbol
## 1 2 5749
## 20012 1 1##
## GOLGA8M
## 5749 2## [1] 20012 8Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "gene_annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "gene_annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"## reactome go_bp
## 1692 7647Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0Conduct enrichment analysis
## [1] 20012 8max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = names(gene_sets)[k]
genes = gene_info$ensembl_gene_id %in% gene_sets[[k]]
names(genes) = gene_info$hgnc_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
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Conduct enrichment analysis
## [1] "PrS_nor_POU2F3_CE_up"
## $reactome
## category over_represented_pvalue
## 743 o glycosylation of tsr domain containing proteins 1.591739e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 743 0.9999987 7 38 0.02110646
##
## $go_bp
## category over_represented_pvalue
## 82 ameboidal type cell migration 2.719625e-11
## 5112 tissue migration 3.096940e-10
## 917 endothelial cell migration 8.572129e-09
## 1687 mesenchyme development 1.041989e-08
## 38 actomyosin structure organization 1.949320e-07
## 4970 sprouting angiogenesis 4.153035e-07
## 403 cell cell signaling by wnt 4.839647e-07
## 1877 muscle tissue development 5.932310e-07
## 1680 mesenchymal cell differentiation 8.013422e-07
## 4901 smad protein signal transduction 1.727102e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 82 1.0000000 31 415 1.446025e-07
## 5112 1.0000000 25 300 8.233216e-07
## 917 1.0000000 19 210 1.385064e-05
## 1687 1.0000000 23 297 1.385064e-05
## 38 1.0000000 17 200 2.072907e-04
## 4970 0.9999999 13 124 3.676058e-04
## 403 0.9999999 25 434 3.676058e-04
## 1877 0.9999998 24 400 3.942762e-04
## 1680 0.9999998 18 240 4.734152e-04
## 4901 0.9999998 10 75 9.183003e-04
##
## [1] "PrS_nor_POU2F3_CE_down"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 129 cardiac conduction 3.106446e-05 0.9999977
## 666 muscle contraction 4.888954e-05 0.9999950
## numDEInCat numInCat FDR
## 129 6 122 0.03241377
## 666 7 193 0.03241377
##
## $go_bp
## category over_represented_pvalue
## 3396 potassium ion homeostasis 8.200227e-06
## 1358 inorganic ion import across plasma membrane 1.443782e-05
## 4923 sodium ion export across plasma membrane 2.116157e-05
## 1333 import across plasma membrane 2.446447e-05
## 1411 intracellular potassium ion homeostasis 2.594676e-05
## 3397 potassium ion import across plasma membrane 3.204801e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 3396 0.9999998 4 28 0.02759179
## 1358 0.9999991 6 117 0.02759179
## 4923 0.9999998 3 12 0.02759179
## 1333 0.9999977 7 189 0.02759179
## 1411 0.9999997 3 13 0.02759179
## 3397 0.9999990 4 40 0.02839988
##
## [1] "PrS_nor_PPARG_CE_up"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 551 intraflagellar transport 1.789545e-05 0.9999965
## numDEInCat numInCat FDR
## 551 14 49 0.02372936
##
## $go_bp
## category over_represented_pvalue
## 18 actin filament organization 1.506530e-08
## 38 actomyosin structure organization 1.351979e-07
## 3641 regulation of actin filament based process 1.353706e-07
## 1239 heart morphogenesis 1.782490e-07
## 4911 smoothened signaling pathway 4.385962e-07
## 629 cilium organization 4.112483e-06
## 371 cartilage development 4.536120e-06
## 659 connective tissue development 4.610018e-06
## 1687 mesenchyme development 5.199423e-06
## 1877 muscle tissue development 6.634200e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 18 1.0000000 73 441 0.0000801022
## 38 1.0000000 41 200 0.0002369375
## 3641 1.0000000 61 362 0.0002369375
## 1239 1.0000000 49 255 0.0002369375
## 4911 0.9999999 32 143 0.0004664032
## 629 0.9999981 63 413 0.0030639330
## 371 0.9999983 36 188 0.0030639330
## 659 0.9999981 46 263 0.0030639330
## 1687 0.9999978 50 297 0.0030717037
## 1877 0.9999969 62 400 0.0035274040
##
## [1] "PrS_nor_PPARG_CE_down"
## $reactome
## category over_represented_pvalue
## 947 response of eif2ak1 hri to heme deficiency 1.427068e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 947 0.9999988 9 15 0.01892293
##
## $go_bp
## category over_represented_pvalue
## 2016 negative regulation of cell substrate adhesion 1.259623e-06
## 4056 regulation of lipid localization 4.251012e-06
## 3066 positive regulation of lipid metabolic process 5.731349e-06
## 4891 skeletal muscle organ development 1.109147e-05
## 3482 protein localization to cell periphery 1.226713e-05
## 3065 positive regulation of lipid localization 1.391728e-05
## 456 cellular ketone metabolic process 1.525635e-05
## 3063 positive regulation of lipid catabolic process 1.664113e-05
## 2182 negative regulation of mapk cascade 2.072601e-05
## 2601 organic anion transport 2.092906e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2016 0.9999997 20 55 0.006697414
## 4056 0.9999984 37 151 0.009854943
## 3066 0.9999980 33 130 0.009854943
## 4891 0.9999955 39 169 0.009854943
## 3482 0.9999939 65 341 0.009854943
## 3065 0.9999955 27 100 0.009854943
## 456 0.9999934 43 198 0.009854943
## 3063 0.9999978 11 24 0.009854943
## 2182 0.9999917 36 155 0.009854943
## 2601 0.9999889 72 391 0.009854943
##
## [1] "PrS_nor_PPARG_KO_up"
## $go_bp
## category
## 5000 striated muscle tissue development
## 1687 mesenchyme development
## 1680 mesenchymal cell differentiation
## 2955 positive regulation of epithelial to mesenchymal transition
## 361 cardiac septum morphogenesis
## 3897 regulation of epithelial to mesenchymal transition
## 954 epithelial to mesenchymal transition
## 1877 muscle tissue development
## 18 actin filament organization
## 2610 ossification
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5000 2.945467e-09 1 38 241
## 1687 9.993698e-09 1 42 297
## 1680 1.138978e-08 1 37 240
## 2955 1.831744e-08 1 16 55
## 361 1.911867e-08 1 19 71
## 3897 5.610694e-08 1 21 97
## 954 5.959661e-08 1 28 161
## 1877 6.947748e-08 1 49 400
## 18 9.102246e-08 1 51 441
## 2610 9.577910e-08 1 48 392
## FDR
## 5000 1.566105e-05
## 1687 2.018649e-05
## 1680 2.018649e-05
## 2955 2.033079e-05
## 361 2.033079e-05
## 3897 4.526788e-05
## 954 4.526788e-05
## 1877 4.617647e-05
## 18 5.092575e-05
## 2610 5.092575e-05
##
## [1] "PrS_nor_PPARG_KO_down"
## $go_bp
## category over_represented_pvalue
## 4056 regulation of lipid localization 1.540138e-06
## 450 cellular component maintenance 5.108457e-06
## 4923 sodium ion export across plasma membrane 5.878393e-06
## 3066 positive regulation of lipid metabolic process 7.478897e-06
## 5297 vitamin metabolic process 7.577194e-06
## 3065 positive regulation of lipid localization 1.079129e-05
## 5241 vascular transport 1.389572e-05
## 456 cellular ketone metabolic process 1.508202e-05
## 1180 glycerolipid biosynthetic process 1.822499e-05
## 3063 positive regulation of lipid catabolic process 2.097258e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4056 0.9999995 29 151 0.008057588
## 450 0.9999989 17 68 0.008057588
## 4923 0.9999997 7 12 0.008057588
## 3066 0.9999977 25 130 0.008057588
## 5297 0.9999980 21 99 0.008057588
## 3065 0.9999970 21 100 0.009562880
## 5241 0.9999964 19 86 0.010023888
## 456 0.9999943 32 198 0.010023888
## 1180 0.9999926 36 237 0.010766918
## 3063 0.9999977 9 24 0.011151121
##
## [1] "PrS_nor_PPARG_PTC_up"
## $reactome
## category
## 147 cell cycle checkpoints
## 654 mitotic spindle checkpoint
## 944 resolution of sister chromatid cohesion
## 960 rho gtpases activate formins
## 958 rho gtpase effectors
## 593 m phase
## 255 deposition of new cenpa containing nucleosomes at the centromere
## 652 mitotic prometaphase
## 274 diseases of programmed cell death
## 191 condensation of prophase chromosomes
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 147 8.971731e-14 1 58 288
## 654 1.226406e-11 1 31 110
## 944 1.344656e-11 1 33 122
## 960 6.501111e-11 1 34 136
## 958 2.556359e-10 1 55 316
## 593 3.047557e-10 1 65 410
## 255 4.467555e-10 1 22 71
## 652 2.832784e-09 1 40 199
## 274 1.617981e-08 1 25 103
## 191 1.488018e-07 1 19 72
## FDR
## 147 1.189652e-10
## 654 5.943380e-09
## 944 5.943380e-09
## 960 2.155118e-08
## 958 6.735102e-08
## 593 6.735102e-08
## 255 8.462825e-08
## 652 4.695339e-07
## 274 2.383825e-06
## 191 1.808518e-05
##
## $go_bp
## category over_represented_pvalue
## 1789 mitotic nuclear division 5.122981e-13
## 1793 mitotic sister chromatid segregation 1.344423e-12
## 4209 regulation of nuclear division 1.505956e-12
## 2005 negative regulation of cell cycle process 1.637366e-12
## 409 cell cycle checkpoint signaling 1.664573e-12
## 4885 sister chromatid segregation 2.134660e-12
## 2002 negative regulation of cell cycle 7.969800e-12
## 2196 negative regulation of mitotic cell cycle 1.298933e-11
## 2592 organelle fission 1.591393e-11
## 3811 regulation of chromosome segregation 1.619315e-11
## under_represented_pvalue numDEInCat numInCat FDR
## 1789 1 56 273 1.770107e-09
## 1793 1 44 186 1.770107e-09
## 4209 1 36 136 1.770107e-09
## 2005 1 57 290 1.770107e-09
## 409 1 44 190 1.770107e-09
## 4885 1 49 225 1.891664e-09
## 2002 1 65 366 6.053632e-09
## 2196 1 47 223 8.609898e-09
## 2592 1 75 461 8.609898e-09
## 3811 1 33 125 8.609898e-09
##
## [1] "PrS_nor_PPARG_PTC_down"
## $go_bp
## category over_represented_pvalue
## 456 cellular ketone metabolic process 2.671879e-08
## 4056 regulation of lipid localization 3.417867e-08
## 4891 skeletal muscle organ development 1.243865e-07
## 3065 positive regulation of lipid localization 8.967724e-07
## 3066 positive regulation of lipid metabolic process 1.148270e-06
## 3063 positive regulation of lipid catabolic process 1.438808e-06
## 1167 glucose metabolic process 2.879317e-06
## 2016 negative regulation of cell substrate adhesion 4.047215e-06
## 5241 vascular transport 4.627484e-06
## 4057 regulation of lipid metabolic process 5.894932e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 456 1.0000000 49 198 0.0000908640
## 4056 1.0000000 41 151 0.0000908640
## 4891 1.0000000 43 169 0.0002204543
## 3065 0.9999997 29 100 0.0011920347
## 3066 0.9999996 34 130 0.0012210703
## 3063 0.9999998 12 24 0.0012750238
## 1167 0.9999989 40 174 0.0021870472
## 2016 0.9999991 19 55 0.0026898805
## 5241 0.9999987 25 86 0.0027338148
## 4057 0.9999973 60 306 0.0030042788
##
## [1] "PrS_nor_GCM1_CE_up"
## $reactome
## category
## 467 hdacs deacetylate histones
## 283 dna methylation
## 1126 sirt1 negatively regulates rrna expression
## 191 condensation of prophase chromosomes
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 828 prc2 methylates histones and dna
## 607 meiotic recombination
## 87 assembly of the orc complex at the origin of replication
## 165 chromatin modifications during the maternal to zygotic transition mzt
## 330 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 467 7.467982e-35 1 56 92
## 283 1.590650e-31 1 44 63
## 1126 2.969744e-30 1 44 66
## 191 3.474557e-30 1 46 72
## 13 2.531680e-29 1 43 65
## 828 2.746975e-29 1 45 71
## 607 3.315912e-29 1 49 84
## 87 1.620033e-28 1 43 67
## 165 1.391507e-27 1 43 69
## 330 4.268360e-27 1 44 74
## FDR
## 467 9.902545e-32
## 283 1.054601e-28
## 1126 1.151816e-27
## 191 1.151816e-27
## 13 6.070815e-27
## 828 6.070815e-27
## 607 6.281284e-27
## 87 2.685204e-26
## 165 2.050153e-25
## 330 5.659845e-25
##
## $go_bp
## category
## 2553 nucleosome organization
## 3484 protein localization to cenp a containing chromatin
## 3450 protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 199 attachment of spindle microtubules to kinetochore
## 4885 sister chromatid segregation
## 2184 negative regulation of megakaryocyte differentiation
## 624 chromosome segregation
## 3763 regulation of cell cycle phase transition
## 3811 regulation of chromosome segregation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553 1.960784e-16 1 45 124
## 3484 1.231137e-13 1 15 18
## 3450 3.393736e-13 1 56 213
## 3487 4.508414e-12 1 21 40
## 199 7.987326e-10 1 21 49
## 4885 2.873941e-09 1 51 225
## 2184 4.100465e-09 1 12 18
## 624 5.219533e-09 1 78 420
## 3763 9.010007e-09 1 76 412
## 3811 9.772371e-09 1 34 125
## FDR
## 2553 1.042549e-12
## 3484 3.272978e-10
## 3450 6.014832e-10
## 3487 5.992809e-09
## 199 8.493722e-07
## 4885 2.546791e-06
## 2184 3.114596e-06
## 624 3.469032e-06
## 3763 5.195969e-06
## 3811 5.195969e-06
##
## [1] "PrS_nor_GCM1_CE_down"
## $reactome
## category over_represented_pvalue
## 1301 unfolded protein response upr 6.696299e-07
## 562 ire1alpha activates chaperones 3.020741e-06
## 630 metal ion slc transporters 3.595884e-05
## 1325 zinc transporters 3.657054e-05
## 1309 vegfr2 mediated vascular permeability 4.496027e-05
## 1121 signaling by vegf 4.582928e-05
## 1212 thyroxine biosynthesis 7.274400e-05
## 493 hsf1 dependent transactivation 1.125618e-04
## 270 diseases of glycosylation 1.503761e-04
## 225 cytosolic trna aminoacylation 3.217039e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 0.9999998 33 93 0.0008879293
## 562 0.9999993 21 50 0.0020027515
## 630 0.9999948 12 23 0.0101282702
## 1325 0.9999969 9 14 0.0101282702
## 1309 0.9999924 13 27 0.0101282702
## 1121 0.9999827 32 105 0.0101282702
## 1212 0.9999982 6 7 0.0137797918
## 493 0.9999746 15 36 0.0186571231
## 270 0.9999332 38 136 0.0221554183
## 225 0.9999406 11 24 0.0392703761
##
## $go_bp
## category
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 560 cellular response to vascular endothelial growth factor stimulus
## 4612 response to endoplasmic reticulum stress
## 1680 mesenchymal cell differentiation
## 4540 regulation of wound healing
## 1421 intrinsic apoptotic signaling pathway
## 4722 response to topologically incorrect protein
## 1687 mesenchyme development
## 954 epithelial to mesenchymal transition
## 1867 muscle cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1425 6.707480e-07 0.9999998 24 60
## 560 1.101408e-06 0.9999997 24 61
## 4612 5.270650e-06 0.9999978 62 255
## 1680 5.329970e-06 0.9999976 60 240
## 4540 8.446621e-06 0.9999969 35 117
## 1421 9.492179e-06 0.9999953 69 297
## 4722 1.037098e-05 0.9999958 42 155
## 1687 1.674066e-05 0.9999916 69 297
## 954 2.034271e-05 0.9999913 43 161
## 1867 2.771449e-05 0.9999848 82 374
## FDR
## 1425 0.002928094
## 560 0.002928094
## 4612 0.007084863
## 1680 0.007084863
## 4540 0.007877503
## 1421 0.007877503
## 4722 0.007877503
## 1687 0.011126261
## 954 0.012018020
## 1867 0.014735792
##
## [1] "PrS_nor_GCM1_KO_up"
## $reactome
## category
## 467 hdacs deacetylate histones
## 283 dna methylation
## 191 condensation of prophase chromosomes
## 1126 sirt1 negatively regulates rrna expression
## 828 prc2 methylates histones and dna
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 157 cellular senescence
## 87 assembly of the orc complex at the origin of replication
## 758 oxidative stress induced senescence
## 165 chromatin modifications during the maternal to zygotic transition mzt
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 467 1.972722e-31 1 50 92
## 283 1.879015e-30 1 41 63
## 191 1.577704e-29 1 43 72
## 1126 2.403441e-29 1 41 66
## 828 1.385737e-28 1 42 71
## 13 2.296409e-28 1 40 65
## 157 1.033815e-27 1 69 194
## 87 1.192736e-27 1 40 67
## 758 1.574478e-27 1 54 122
## 165 8.599933e-27 1 40 69
## FDR
## 467 2.615829e-28
## 283 1.245787e-27
## 191 6.973453e-27
## 1126 7.967407e-27
## 828 3.674975e-26
## 13 5.075064e-26
## 157 1.958341e-25
## 87 1.976960e-25
## 758 2.319732e-25
## 165 1.140351e-24
##
## $go_bp
## category
## 2553 nucleosome organization
## 3450 protein dna complex assembly
## 3484 protein localization to cenp a containing chromatin
## 3487 protein localization to chromosome centromeric region
## 2184 negative regulation of megakaryocyte differentiation
## 2592 organelle fission
## 4885 sister chromatid segregation
## 3811 regulation of chromosome segregation
## 4090 regulation of megakaryocyte differentiation
## 1789 mitotic nuclear division
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553 5.195964e-18 1.0000000 43 124
## 3450 1.106062e-13 1.0000000 51 213
## 3484 2.997629e-13 1.0000000 14 18
## 3487 1.323141e-12 1.0000000 20 40
## 2184 8.944542e-09 1.0000000 11 18
## 2592 1.021363e-08 1.0000000 72 461
## 4885 3.638216e-08 1.0000000 43 225
## 3811 7.897609e-08 1.0000000 29 125
## 4090 1.776750e-07 1.0000000 14 36
## 1789 2.614751e-07 0.9999999 47 273
## FDR
## 2553 2.762694e-14
## 3450 2.940466e-10
## 3484 5.312798e-10
## 3487 1.758786e-09
## 2184 9.050974e-06
## 2592 9.050974e-06
## 4885 2.763485e-05
## 3811 5.248948e-05
## 4090 1.049665e-04
## 1789 1.368058e-04
##
## [1] "PrS_nor_GCM1_KO_down"
## $reactome
## category
## 630 metal ion slc transporters
## 1325 zinc transporters
## 270 diseases of glycosylation
## 1200 tfap2 ap 2 family regulates transcription of growth factors and their receptors
## 1121 signaling by vegf
## 263 diseases associated with glycosaminoglycan metabolism
## 93 attachment and entry
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 630 3.535974e-05 0.9999951 11 23
## 1325 8.008108e-05 0.9999927 8 14
## 270 9.946459e-05 0.9999585 34 136
## 1200 1.369956e-04 0.9999857 8 15
## 1121 1.567498e-04 0.9999403 27 105
## 263 1.787301e-04 0.9999586 14 38
## 93 2.626798e-04 0.9999625 9 19
## FDR
## 630 0.03949936
## 1325 0.03949936
## 270 0.03949936
## 1200 0.03949936
## 1121 0.03949936
## 263 0.03949936
## 93 0.04975905
##
## $go_bp
## category
## 4269 regulation of polysaccharide metabolic process
## 2774 polysaccharide metabolic process
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 371 cartilage development
## 560 cellular response to vascular endothelial growth factor stimulus
## 612 chondrocyte differentiation
## 659 connective tissue development
## 2108 negative regulation of growth
## 2376 negative regulation of transport
## 4050 regulation of leukocyte proliferation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4269 1.125419e-06 0.9999998 17 40
## 2774 3.300126e-06 0.9999990 27 90
## 1425 8.325300e-06 0.9999980 20 60
## 371 1.203553e-05 0.9999949 43 188
## 560 1.288100e-05 0.9999967 20 61
## 612 1.514156e-05 0.9999947 30 114
## 659 1.581880e-05 0.9999926 55 263
## 2108 1.665980e-05 0.9999925 49 230
## 2376 2.311529e-05 0.9999877 72 383
## 4050 2.367817e-05 0.9999893 47 219
## FDR
## 4269 0.005983854
## 2774 0.008773384
## 1425 0.011072518
## 371 0.011072518
## 560 0.011072518
## 612 0.011072518
## 659 0.011072518
## 2108 0.011072518
## 2376 0.012057352
## 4050 0.012057352
##
## [1] "PrS_nor_GCM1_PTC_up"
## $reactome
## category
## 467 hdacs deacetylate histones
## 283 dna methylation
## 828 prc2 methylates histones and dna
## 191 condensation of prophase chromosomes
## 758 oxidative stress induced senescence
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 1126 sirt1 negatively regulates rrna expression
## 87 assembly of the orc complex at the origin of replication
## 157 cellular senescence
## 1043 senescence associated secretory phenotype sasp
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 467 1.465736e-27 1 44 92
## 283 2.188595e-26 1 36 63
## 828 5.080876e-25 1 37 71
## 191 8.734610e-25 1 37 72
## 758 1.116688e-24 1 48 122
## 13 1.590379e-24 1 35 65
## 1126 2.710157e-24 1 35 66
## 87 5.985216e-24 1 35 67
## 157 6.521321e-24 1 60 194
## 1043 1.899892e-23 1 44 110
## FDR
## 467 1.943566e-24
## 283 1.451039e-23
## 828 2.245747e-22
## 191 2.895523e-22
## 758 2.961457e-22
## 13 3.514737e-22
## 1126 5.133812e-22
## 87 9.608080e-22
## 157 9.608080e-22
## 1043 2.519256e-21
##
## $go_bp
## category
## 2553 nucleosome organization
## 3484 protein localization to cenp a containing chromatin
## 3450 protein dna complex assembly
## 3487 protein localization to chromosome centromeric region
## 2184 negative regulation of megakaryocyte differentiation
## 4090 regulation of megakaryocyte differentiation
## 3485 protein localization to chromatin
## 4161 regulation of myeloid cell differentiation
## 5087 telomere organization
## 2213 negative regulation of myeloid cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2553 5.094182e-17 1.0000000 39 124
## 3484 5.520787e-16 1.0000000 15 18
## 3450 1.072808e-13 1.0000000 47 213
## 3487 1.355066e-11 1.0000000 18 40
## 2184 6.666303e-11 1.0000000 12 18
## 4090 2.731074e-09 1.0000000 15 36
## 3485 7.851264e-09 1.0000000 19 59
## 4161 1.489780e-08 1.0000000 36 187
## 5087 9.548740e-08 1.0000000 34 187
## 2213 5.596545e-07 0.9999999 20 83
## FDR
## 2553 2.708577e-13
## 3484 1.467701e-12
## 3450 1.901373e-10
## 3487 1.801222e-08
## 2184 7.088946e-08
## 4090 2.420187e-06
## 3485 5.963596e-06
## 4161 9.901451e-06
## 5087 5.641184e-05
## 2213 2.975683e-04
##
## [1] "PrS_nor_GCM1_PTC_down"
## $reactome
## category
## 630 metal ion slc transporters
## 1325 zinc transporters
## 1200 tfap2 ap 2 family regulates transcription of growth factors and their receptors
## 774 peptide hormone biosynthesis
## 1121 signaling by vegf
## 263 diseases associated with glycosaminoglycan metabolism
## 1118 signaling by tgfb family members
## 270 diseases of glycosylation
## 93 attachment and entry
## 1301 unfolded protein response upr
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 630 4.028729e-05 0.9999943 11 23
## 1325 8.924555e-05 0.9999917 8 14
## 1200 1.547397e-04 0.9999835 8 15
## 774 1.883732e-04 0.9999840 7 12
## 1121 1.916607e-04 0.9999260 27 105
## 263 1.918146e-04 0.9999553 14 38
## 1118 2.366128e-04 0.9999018 30 122
## 270 2.667070e-04 0.9998833 33 136
## 93 2.751037e-04 0.9999604 9 19
## 1301 3.330896e-04 0.9998745 24 93
## FDR
## 630 0.04053195
## 1325 0.04053195
## 1200 0.04053195
## 774 0.04053195
## 1121 0.04053195
## 263 0.04053195
## 1118 0.04053195
## 270 0.04053195
## 93 0.04053195
## 1301 0.04399558
##
## $go_bp
## category
## 254 biomineral tissue development
## 560 cellular response to vascular endothelial growth factor stimulus
## 4269 regulation of polysaccharide metabolic process
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 2774 polysaccharide metabolic process
## 1680 mesenchymal cell differentiation
## 612 chondrocyte differentiation
## 611 chondrocyte development
## 5308 wound healing
## 1867 muscle cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 254 3.638446e-07 0.9999999 42 158
## 560 9.797003e-07 0.9999998 22 61
## 4269 1.382109e-06 0.9999998 17 40
## 1425 2.689562e-06 0.9999994 21 60
## 2774 4.364221e-06 0.9999987 27 90
## 1680 6.254918e-06 0.9999973 53 240
## 612 6.945796e-06 0.9999976 31 114
## 611 7.828736e-06 0.9999987 14 32
## 5308 7.947119e-06 0.9999961 76 389
## 1867 7.949952e-06 0.9999961 74 374
## FDR
## 254 0.001934562
## 560 0.002449559
## 4269 0.002449559
## 1425 0.003575101
## 2774 0.004226989
## 1680 0.004226989
## 612 0.004226989
## 611 0.004226989
## 5308 0.004226989
## 1867 0.004226989
##
## [1] "PrS_nor_FOSB_KO_up"
## $reactome
## category
## 518 integrin cell surface interactions
## 346 extracellular matrix organization
## 185 collagen degradation
## 85 assembly of collagen fibrils and other multimeric structures
## 184 collagen chain trimerization
## 186 collagen formation
## 183 collagen biosynthesis and modifying enzymes
## 307 ecm proteoglycans
## 40 adherens junctions interactions
## 253 degradation of the extracellular matrix
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 518 1.656022e-08 1.0000000 10 78
## 346 3.431410e-08 1.0000000 17 285
## 185 5.401527e-07 1.0000000 8 60
## 85 6.310812e-07 1.0000000 8 60
## 184 6.873574e-07 1.0000000 7 42
## 186 1.044059e-06 0.9999999 9 88
## 183 1.169812e-06 0.9999999 8 65
## 307 3.281918e-06 0.9999997 8 75
## 40 4.041532e-06 0.9999997 7 53
## 253 4.337458e-06 0.9999995 10 134
## FDR
## 518 2.195885e-05
## 346 2.275025e-05
## 185 1.822872e-04
## 85 1.822872e-04
## 184 1.822872e-04
## 186 2.215958e-04
## 183 2.215958e-04
## 307 5.439778e-04
## 40 5.751469e-04
## 253 5.751469e-04
##
## $go_bp
## category over_represented_pvalue
## 645 collagen fibril organization 3.354659e-10
## 1022 external encapsulating structure organization 2.492030e-09
## 371 cartilage development 3.236358e-07
## 82 ameboidal type cell migration 3.520497e-07
## 659 connective tissue development 6.059314e-07
## 612 chondrocyte differentiation 9.895230e-07
## 322 canonical wnt signaling pathway 2.037041e-06
## 1687 mesenchyme development 2.729083e-06
## 1239 heart morphogenesis 3.501847e-06
## 4997 striated muscle cell differentiation 4.598044e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 645 1.0000000 11 63 1.783672e-06
## 1022 1.0000000 19 302 6.625063e-06
## 371 1.0000000 13 188 4.679621e-04
## 82 0.9999999 19 415 4.679621e-04
## 659 0.9999999 15 263 6.443475e-04
## 612 0.9999999 10 114 8.768823e-04
## 322 0.9999996 15 295 1.547278e-03
## 1687 0.9999995 15 297 1.813817e-03
## 1239 0.9999994 14 255 2.068814e-03
## 4997 0.9999991 14 274 2.243809e-03
##
## [1] "PrS_nor_FOSB_PTC_up"
## $reactome
## category
## 346 extracellular matrix organization
## 518 integrin cell surface interactions
## 307 ecm proteoglycans
## 183 collagen biosynthesis and modifying enzymes
## 184 collagen chain trimerization
## 253 degradation of the extracellular matrix
## 185 collagen degradation
## 186 collagen formation
## 85 assembly of collagen fibrils and other multimeric structures
## 1163 syndecan interactions
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 346 1.436869e-11 1.0000000 29 285
## 518 1.755802e-09 1.0000000 14 78
## 307 2.243631e-08 1.0000000 13 75
## 183 4.031943e-08 1.0000000 12 65
## 184 4.467943e-08 1.0000000 10 42
## 253 9.915951e-08 1.0000000 16 134
## 185 1.356254e-07 1.0000000 11 60
## 186 1.464910e-07 1.0000000 13 88
## 85 1.620152e-06 0.9999998 10 60
## 1163 3.499459e-06 0.9999998 7 27
## FDR
## 346 1.905289e-08
## 518 1.164097e-06
## 307 9.916849e-06
## 183 1.184899e-05
## 184 1.184899e-05
## 253 2.191425e-05
## 185 2.428089e-05
## 186 2.428089e-05
## 85 2.387024e-04
## 1163 4.640283e-04
##
## $go_bp
## category over_represented_pvalue
## 1022 external encapsulating structure organization 1.925057e-14
## 1239 heart morphogenesis 1.519626e-13
## 645 collagen fibril organization 1.967602e-12
## 1687 mesenchyme development 1.713638e-11
## 659 connective tissue development 2.538679e-11
## 371 cartilage development 6.821165e-11
## 1877 muscle tissue development 8.150329e-11
## 5000 striated muscle tissue development 9.504090e-11
## 82 ameboidal type cell migration 4.903542e-10
## 1680 mesenchymal cell differentiation 5.439706e-10
## under_represented_pvalue numDEInCat numInCat FDR
## 1022 1 34 302 1.023553e-10
## 1239 1 31 255 4.039925e-10
## 645 1 16 63 3.487247e-09
## 1687 1 30 297 2.277853e-08
## 659 1 28 263 2.699632e-08
## 371 1 23 188 6.044689e-08
## 1877 1 34 400 6.190757e-08
## 5000 1 26 241 6.316656e-08
## 82 1 33 415 2.892291e-07
## 1680 1 25 240 2.892291e-07
##
## [1] "PrS_nor_FOSB_PTC_down"
## $reactome
## category over_represented_pvalue
## 762 p75 ntr receptor mediated signalling 1.338713e-05
## 148 cell death signalling via nrage nrif and nade 3.781977e-05
## 399 g alpha 12 13 signalling events 4.948099e-05
## 725 nrage signals death through jnk 1.312017e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 762 0.9999989 7 97 0.01775133
## 148 0.9999971 6 76 0.02187060
## 399 0.9999960 6 80 0.02187060
## 725 0.9999907 5 59 0.04349338
##
## [1] "PrS_nor_EPAS1_CE_up"
## $reactome
## category over_represented_pvalue
## 277 dissolution of fibrin clot 2.198485e-05
## 618 metabolism of carbohydrates 5.363641e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 277 0.9999991 5 13 0.02915191
## 618 0.9999822 22 284 0.03556094
##
## $go_bp
## category over_represented_pvalue
## 1055 fatty acid metabolic process 3.613651e-06
## 488 cellular response to decreased oxygen levels 6.688351e-06
## 1421 intrinsic apoptotic signaling pathway 7.550311e-06
## 1167 glucose metabolic process 1.379079e-05
## 499 cellular response to fatty acid 1.400568e-05
## 4619 response to fatty acid 1.535808e-05
## 3613 pyruvate metabolic process 1.586226e-05
## 531 cellular response to oxygen levels 2.041856e-05
## 1827 monosaccharide metabolic process 2.666690e-05
## 2753 plasminogen activation 3.111105e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1055 0.9999988 27 352 0.01204852
## 488 0.9999985 16 142 0.01204852
## 1421 0.9999976 24 297 0.01204852
## 1167 0.9999966 17 174 0.01204852
## 499 0.9999989 7 29 0.01204852
## 4619 0.9999981 9 50 0.01204852
## 3613 0.9999969 13 108 0.01204852
## 531 0.9999950 16 156 0.01357069
## 1827 0.9999920 20 241 0.01571608
## 2753 0.9999979 6 23 0.01571608
##
## [1] "PrS_nor_EPAS1_CE_down"
## $reactome
## category
## 13 activated pkn1 stimulates transcription of ar androgen receptor regulated genes klk2 and klk3
## 191 condensation of prophase chromosomes
## 467 hdacs deacetylate histones
## 1043 senescence associated secretory phenotype sasp
## 829 pre notch expression and processing
## 466 hcmv late events
## 986 rmts methylate histone arginines
## 606 meiosis
## 608 meiotic synapsis
## 283 dna methylation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 13 1.595702e-06 0.9999999 9 65
## 191 4.361946e-06 0.9999995 9 72
## 467 4.562914e-06 0.9999994 10 92
## 1043 4.630293e-06 0.9999993 11 110
## 829 4.796600e-06 0.9999993 11 107
## 466 6.814211e-06 0.9999990 11 114
## 986 8.902286e-06 0.9999990 9 76
## 606 1.150517e-05 0.9999982 11 114
## 608 1.230217e-05 0.9999985 9 75
## 283 1.257684e-05 0.9999987 8 63
## FDR
## 13 0.001272058
## 191 0.001272058
## 467 0.001272058
## 1043 0.001272058
## 829 0.001272058
## 466 0.001505941
## 986 0.001667688
## 606 0.001667688
## 608 0.001667688
## 283 0.001667688
##
## [1] "PrS_nor_EPAS1_PTC_up"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 277 dissolution of fibrin clot 1.196543e-05 0.9999999
## numDEInCat numInCat FDR
## 277 3 13 0.01586616
##
## $go_bp
## category
## 2753 plasminogen activation
## 5308 wound healing
## 4352 regulation of release of cytochrome c from mitochondria
## 3930 regulation of fibrinolysis
## 1531 liposaccharide metabolic process
## 4263 regulation of plasminogen activation
## 5317 zymogen activation
## 4545 release of cytochrome c from mitochondria
## 2016 negative regulation of cell substrate adhesion
## 4540 regulation of wound healing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2753 1.171197e-06 1.0000000 4 23
## 5308 7.274508e-06 0.9999992 9 389
## 4352 1.549539e-05 0.9999996 4 43
## 3930 2.743100e-05 0.9999997 3 17
## 1531 2.899217e-05 0.9999985 5 102
## 4263 3.289378e-05 0.9999996 3 18
## 5317 3.309511e-05 0.9999990 4 52
## 4545 3.857676e-05 0.9999987 4 54
## 2016 4.024798e-05 0.9999987 4 55
## 4540 5.490820e-05 0.9999968 5 117
## FDR
## 2753 0.006227254
## 5308 0.019339280
## 4352 0.023777610
## 3930 0.023777610
## 1531 0.023777610
## 4263 0.023777610
## 5317 0.023777610
## 4545 0.023777610
## 2016 0.023777610
## 4540 0.029194690
##
## [1] "PrS_nor_GRHL1_CE_up"
## $reactome
## category over_represented_pvalue
## 525 interferon alpha beta signaling 2.262603e-10
## 526 interferon gamma signaling 2.184318e-07
## 527 interferon signaling 3.661905e-07
## 184 collagen chain trimerization 8.682218e-05
## 307 ecm proteoglycans 1.229151e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 525 1.0000000 18 65 3.000212e-07
## 526 1.0000000 16 81 1.448203e-04
## 527 0.9999999 29 242 1.618562e-04
## 184 0.9999869 9 42 2.878155e-02
## 307 0.9999731 12 75 3.259707e-02
##
## $go_bp
## category over_represented_pvalue
## 2397 negative regulation of viral genome replication 4.301158e-08
## 4644 response to interferon beta 1.591006e-07
## 513 cellular response to interferon beta 1.932150e-07
## 2400 negative regulation of viral process 4.248355e-07
## 4727 response to type i interferon 9.094625e-07
## 1374 interferon mediated signaling pathway 1.127029e-06
## 4901 smad protein signal transduction 1.388827e-06
## 717 defense response to symbiont 3.844608e-06
## 1687 mesenchyme development 1.006543e-05
## 4734 response to virus 1.403765e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2397 1.0000000 14 52 0.0002286926
## 4644 1.0000000 10 31 0.0003424413
## 513 1.0000000 9 24 0.0003424413
## 2400 0.9999999 16 81 0.0005647125
## 4727 0.9999998 15 74 0.0009671225
## 1374 0.9999998 16 87 0.0009987356
## 4901 0.9999998 15 75 0.0010549134
## 717 0.9999987 31 289 0.0025552229
## 1687 0.9999963 31 297 0.0059464333
## 4734 0.9999944 35 375 0.0074638180
##
## [1] "PrS_nor_GRHL1_CE_down"
## $reactome
## category
## 80 asparagine n linked glycosylation
## 493 hsf1 dependent transactivation
## 1301 unfolded protein response upr
## 1200 tfap2 ap 2 family regulates transcription of growth factors and their receptors
## 562 ire1alpha activates chaperones
## 774 peptide hormone biosynthesis
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 80 1.302512e-05 0.9999942 47 300
## 493 2.373316e-05 0.9999961 12 36
## 1301 6.369956e-05 0.9999807 20 93
## 1200 8.902948e-05 0.9999922 7 15
## 562 1.516482e-04 0.9999653 13 50
## 774 1.853290e-04 0.9999861 6 12
## FDR
## 80 0.01573509
## 493 0.01573509
## 1301 0.02815520
## 1200 0.02951327
## 562 0.04021711
## 774 0.04095770
##
## $go_bp
## category over_represented_pvalue
## 4612 response to endoplasmic reticulum stress 2.119732e-07
## 963 erad pathway 2.749650e-06
## 885 endocrine hormone secretion 3.203522e-06
## 477 cellular response to biotic stimulus 4.607135e-06
## 1299 hormone transport 7.020740e-06
## 3482 protein localization to cell periphery 8.115957e-06
## 4642 response to insulin 9.500709e-06
## 3536 protein refolding 1.147332e-05
## 3510 protein localization to plasma membrane 1.259720e-05
## 3690 regulation of autophagy 1.379981e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4612 0.9999999 45 255 0.001127061
## 963 0.9999992 24 108 0.005677709
## 885 0.9999994 16 54 0.005677709
## 477 0.9999982 37 211 0.006124035
## 1299 0.9999970 46 292 0.007192091
## 3482 0.9999964 51 341 0.007192091
## 4642 0.9999961 40 244 0.007216467
## 3536 0.9999987 10 25 0.007337361
## 3510 0.9999945 44 283 0.007337361
## 3690 0.9999937 50 341 0.007337361
##
## [1] "PrS_nor_GRHL1_KO_up"
## $reactome
## category over_represented_pvalue
## 525 interferon alpha beta signaling 3.890682e-11
## 184 collagen chain trimerization 6.021122e-07
## 183 collagen biosynthesis and modifying enzymes 1.504942e-06
## 527 interferon signaling 5.177422e-06
## 346 extracellular matrix organization 2.091641e-05
## 518 integrin cell surface interactions 3.927685e-05
## 307 ecm proteoglycans 4.501624e-05
## 186 collagen formation 4.629615e-05
## 526 interferon gamma signaling 4.890721e-05
## 185 collagen degradation 1.132855e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 525 1.0000000 18 65 5.159045e-08
## 184 0.9999999 11 42 3.992004e-04
## 183 0.9999998 13 65 6.651844e-04
## 527 0.9999984 25 242 1.716315e-03
## 346 0.9999926 27 285 5.547032e-03
## 518 0.9999924 12 78 7.205663e-03
## 307 0.9999912 12 75 7.205663e-03
## 186 0.9999901 13 88 7.205663e-03
## 526 0.9999902 12 81 7.205663e-03
## 185 0.9999796 10 60 1.502165e-02
##
## $go_bp
## category
## 2397 negative regulation of viral genome replication
## 4901 smad protein signal transduction
## 2400 negative regulation of viral process
## 1687 mesenchyme development
## 4727 response to type i interferon
## 1374 interferon mediated signaling pathway
## 5158 transmembrane receptor protein serine threonine kinase signaling pathway
## 1870 muscle cell proliferation
## 2166 negative regulation of locomotion
## 1680 mesenchymal cell differentiation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 2397 8.686401e-09 1.0000000 14 52
## 4901 2.550998e-07 1.0000000 15 75
## 2400 4.212869e-07 0.9999999 15 81
## 1687 5.509640e-07 0.9999998 31 297
## 4727 1.038527e-06 0.9999998 14 74
## 1374 1.058408e-06 0.9999998 15 87
## 5158 1.076901e-06 0.9999996 35 359
## 1870 1.329007e-06 0.9999996 23 191
## 2166 2.022586e-06 0.9999993 31 315
## 1680 2.438094e-06 0.9999993 26 240
## FDR
## 2397 4.618559e-05
## 4901 6.781829e-04
## 2400 7.323689e-04
## 1687 7.323689e-04
## 4727 8.179833e-04
## 1374 8.179833e-04
## 5158 8.179833e-04
## 1870 8.832911e-04
## 2166 1.194899e-03
## 1680 1.296335e-03
##
## [1] "PrS_nor_GRHL1_KO_down"
## $go_bp
## category over_represented_pvalue
## 3372 positive regulation of wound healing 3.374043e-07
## 3261 positive regulation of response to wounding 6.796705e-07
## 4873 signal release 1.186191e-05
## 1668 membrane lipid metabolic process 2.258557e-05
## 1299 hormone transport 2.892334e-05
## 4722 response to topologically incorrect protein 3.476257e-05
## 2719 phospholipid metabolic process 3.568355e-05
## 1018 exocytosis 5.470721e-05
## 5308 wound healing 6.424330e-05
## 477 cellular response to biotic stimulus 7.715935e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 3372 1.0000000 14 56 0.001793978
## 3261 0.9999999 15 68 0.001806904
## 4873 0.9999948 43 446 0.021023267
## 1668 0.9999925 24 199 0.027104204
## 1299 0.9999887 31 292 0.027104204
## 4722 0.9999895 20 155 0.027104204
## 2719 0.9999850 35 359 0.027104204
## 1018 0.9999771 33 331 0.036359777
## 5308 0.9999714 37 389 0.037953515
## 477 0.9999722 24 211 0.041025627
##
## [1] "PrS_nor_GRHL1_PTC_up"
## $reactome
## category over_represented_pvalue
## 710 non integrin membrane ecm interactions 7.148400e-10
## 518 integrin cell surface interactions 6.852697e-08
## 958 rho gtpase effectors 2.075012e-07
## 307 ecm proteoglycans 2.652440e-07
## 960 rho gtpases activate formins 9.592101e-07
## 1163 syndecan interactions 1.007292e-06
## 346 extracellular matrix organization 3.722419e-06
## 957 rho gtpase cycle 6.683154e-06
## 1131 smooth muscle contraction 1.189650e-05
## 1042 semaphorin interactions 1.835703e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 710 1.0000000 24 58 9.478779e-07
## 518 1.0000000 25 78 4.543338e-05
## 958 1.0000000 58 316 8.792838e-05
## 307 0.9999999 24 75 8.792838e-05
## 960 0.9999997 32 136 2.226116e-04
## 1163 0.9999999 13 27 2.226116e-04
## 346 0.9999985 54 285 7.051324e-04
## 957 0.9999966 75 450 1.107733e-03
## 1131 0.9999977 15 43 1.752751e-03
## 1042 0.9999955 18 63 2.279380e-03
##
## $go_bp
## category over_represented_pvalue
## 82 ameboidal type cell migration 5.669079e-11
## 38 actomyosin structure organization 1.916489e-10
## 5308 wound healing 3.273662e-10
## 18 actin filament organization 3.986723e-10
## 5112 tissue migration 7.685190e-09
## 16 actin filament bundle organization 3.698749e-08
## 4209 regulation of nuclear division 8.161009e-08
## 4132 regulation of mitotic nuclear division 1.461424e-07
## 1687 mesenchyme development 1.848023e-07
## 2234 negative regulation of nuclear division 2.618742e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 82 1.0000000 85 415 3.014249e-07
## 38 1.0000000 51 200 5.094987e-07
## 5308 1.0000000 79 389 5.299352e-07
## 18 1.0000000 86 441 5.299352e-07
## 5112 1.0000000 63 300 8.172431e-06
## 16 1.0000000 40 158 3.277708e-05
## 4209 1.0000000 34 136 6.198870e-05
## 4132 1.0000000 30 115 9.712992e-05
## 1687 1.0000000 59 297 1.091771e-04
## 2234 0.9999999 20 61 1.392385e-04
##
## [1] "PrS_nor_GRHL1_PTC_down"
## $reactome
## category
## 1301 unfolded protein response upr
## 80 asparagine n linked glycosylation
## 562 ire1alpha activates chaperones
## 91 atf6 atf6 alpha activates chaperone genes
## 1200 tfap2 ap 2 family regulates transcription of growth factors and their receptors
## 947 response of eif2ak1 hri to heme deficiency
## 92 atf6 atf6 alpha activates chaperones
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1301 1.036660e-07 1.0000000 31 93
## 80 2.254689e-06 0.9999991 65 300
## 562 3.077659e-06 0.9999994 19 50
## 91 4.951005e-05 0.9999973 7 10
## 1200 1.433777e-04 0.9999849 8 15
## 947 1.552943e-04 0.9999835 8 15
## 92 2.517765e-04 0.9999775 7 12
## FDR
## 1301 0.0001374611
## 80 0.0013603254
## 562 0.0013603254
## 91 0.0164125812
## 1200 0.0343200368
## 947 0.0343200368
## 92 0.0476936605
##
## $go_bp
## category over_represented_pvalue
## 4612 response to endoplasmic reticulum stress 1.852016e-08
## 3494 protein localization to endoplasmic reticulum 6.279844e-08
## 3216 positive regulation of protein catabolic process 1.656429e-07
## 4642 response to insulin 1.167749e-06
## 1299 hormone transport 2.736726e-06
## 887 endocrine process 4.469054e-06
## 3452 protein exit from endoplasmic reticulum 4.626179e-06
## 4697 response to peptide hormone 6.166372e-06
## 963 erad pathway 1.228118e-05
## 477 cellular response to biotic stimulus 1.234294e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 4612 1.0000000 61 255 9.847171e-05
## 3494 1.0000000 26 72 1.669497e-04
## 3216 1.0000000 50 204 2.935744e-04
## 4642 0.9999996 55 244 1.552230e-03
## 1299 0.9999989 62 292 2.910234e-03
## 887 0.9999987 25 81 3.513913e-03
## 3452 0.9999990 18 49 3.513913e-03
## 4697 0.9999970 76 389 4.098325e-03
## 963 0.9999958 29 108 6.024932e-03
## 477 0.9999946 47 211 6.024932e-03
##
## [1] "PrS_hyp_EPAS1_CE_up"
## $reactome
## category over_represented_pvalue
## 56 amino acids regulate mtorc1 3.500350e-07
## 515 insulin receptor recycling 1.967660e-06
## 1267 transferrin endocytosis and recycling 4.604666e-06
## 1301 unfolded protein response upr 1.369721e-05
## 1121 signaling by vegf 1.902357e-05
## 1006 ros and rns production in phagocytes 3.293891e-05
## 162 cholesterol biosynthesis 5.099474e-05
## 55 amino acid transport across the plasma membrane 5.772631e-05
## 93 attachment and entry 1.148130e-04
## 564 iron uptake and transport 1.422465e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 56 0.9999999 20 54 0.0004641463
## 515 0.9999998 13 28 0.0013045589
## 1267 0.9999994 13 30 0.0020352622
## 1301 0.9999958 25 93 0.0045406251
## 1121 0.9999937 27 105 0.0050450496
## 1006 0.9999940 13 35 0.0072794981
## 162 0.9999921 11 27 0.0095681357
## 55 0.9999899 12 31 0.0095681357
## 93 0.9999854 9 19 0.0169157832
## 564 0.9999623 16 55 0.0188618912
##
## $go_bp
## category
## 4612 response to endoplasmic reticulum stress
## 1578 macroautophagy
## 4078 regulation of macroautophagy
## 5040 synaptic vesicle lumen acidification
## 3452 protein exit from endoplasmic reticulum
## 1425 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress
## 5154 translational initiation
## 4722 response to topologically incorrect protein
## 963 erad pathway
## 3690 regulation of autophagy
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4612 2.144110e-09 1.0000000 57 255
## 1578 1.146466e-07 1.0000000 63 327
## 4078 1.742118e-07 0.9999999 38 156
## 5040 2.408251e-07 1.0000000 10 16
## 3452 4.397676e-07 0.9999999 18 49
## 1425 6.792466e-07 0.9999999 20 60
## 5154 8.717581e-07 0.9999997 30 118
## 4722 8.741577e-07 0.9999997 36 155
## 963 1.521337e-06 0.9999996 28 108
## 3690 1.538510e-06 0.9999995 62 341
## FDR
## 4612 1.140023e-05
## 1578 3.047880e-04
## 4078 3.087613e-04
## 5040 3.201167e-04
## 3452 4.676488e-04
## 1425 5.809870e-04
## 5154 5.809870e-04
## 4722 5.809870e-04
## 963 8.180257e-04
## 3690 8.180257e-04
##
## [1] "PrS_hyp_EPAS1_CE_down"
## $go_bp
## category
## 214 axon guidance
## 5240 vascular process in circulatory system
## 1681 mesenchymal cell migration
## 2417 neural crest cell differentiation
## 2447 neuron projection extension involved in neuron projection guidance
## 1926 negative chemotaxis
## 2006 negative regulation of cell development
## 462 cellular modified amino acid metabolic process
## 2328 negative regulation of smooth muscle cell migration
## 4975 stem cell development
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 214 3.388209e-07 0.9999999 31 222
## 5240 4.660862e-06 0.9999984 31 245
## 1681 5.933271e-06 0.9999990 13 60
## 2417 9.159955e-06 0.9999980 16 91
## 2447 1.848098e-05 0.9999975 10 38
## 1926 1.981031e-05 0.9999969 11 47
## 2006 2.235815e-05 0.9999917 29 253
## 462 4.024245e-05 0.9999892 17 120
## 2328 6.991205e-05 0.9999932 7 22
## 4975 8.733168e-05 0.9999787 14 86
## FDR
## 214 0.001801511
## 5240 0.010515733
## 1681 0.010515733
## 2417 0.012175870
## 2447 0.016982615
## 1926 0.016982615
## 2006 0.016982615
## 462 0.026746141
## 2328 0.041302487
## 4975 0.043010491
##
## [1] "PrS_hyp_EPAS1_KO_up"
## $reactome
## category over_represented_pvalue
## 632 metallothioneins bind metals 2.148456e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 632 0.9999994 5 8 0.02848853
##
## $go_bp
## category over_represented_pvalue
## 1521 lipid import into cell 1.247918e-05
## 4612 response to endoplasmic reticulum stress 2.722863e-05
## 1417 intracellular zinc ion homeostasis 3.169932e-05
## 4050 regulation of leukocyte proliferation 3.624881e-05
## 4540 regulation of wound healing 5.140192e-05
## 18 actin filament organization 5.478638e-05
## 1997 negative regulation of cell adhesion 5.545999e-05
## 2376 negative regulation of transport 5.784322e-05
## 4693 response to oxygen levels 8.077530e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1521 0.9999989 8 20 0.03844405
## 4612 0.9999893 32 255 0.03844405
## 1417 0.9999960 9 30 0.03844405
## 4050 0.9999862 29 219 0.03844405
## 4540 0.9999848 19 117 0.03844405
## 18 0.9999734 47 441 0.03844405
## 1997 0.9999772 32 260 0.03844405
## 2376 0.9999730 42 383 0.03844405
## 4693 0.9999637 37 320 0.04772025
##
## [1] "PrS_hyp_EPAS1_KO_down"
## $reactome
## category over_represented_pvalue
## 184 collagen chain trimerization 1.906102e-06
## 253 degradation of the extracellular matrix 4.166207e-06
## 185 collagen degradation 5.201623e-06
## 183 collagen biosynthesis and modifying enzymes 7.172428e-05
## 186 collagen formation 1.633145e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 184 0.9999998 9 42 0.002299118
## 253 0.9999992 15 134 0.002299118
## 185 0.9999994 10 60 0.002299118
## 183 0.9999890 9 65 0.023776598
## 186 0.9999684 10 88 0.043310997
##
## $go_bp
## category over_represented_pvalue
## 337 cardiac chamber development 5.854137e-08
## 214 axon guidance 6.844080e-08
## 363 cardiac ventricle development 1.208774e-07
## 1681 mesenchymal cell migration 5.382602e-07
## 869 embryonic organ development 8.762555e-07
## 165 appendage morphogenesis 1.321765e-06
## 870 embryonic organ morphogenesis 2.184799e-06
## 4711 response to retinoic acid 3.660770e-06
## 4975 stem cell development 3.780786e-06
## 2567 odontogenesis 5.439896e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 337 1.0000000 20 165 0.0001819499
## 214 1.0000000 23 222 0.0001819499
## 363 1.0000000 17 124 0.0002142351
## 1681 0.9999999 11 60 0.0007154824
## 869 0.9999997 31 424 0.0009318101
## 165 0.9999997 16 141 0.0011713043
## 870 0.9999994 23 271 0.0016595106
## 4711 0.9999994 13 99 0.0022336041
## 4975 0.9999994 12 86 0.0022336041
## 2567 0.9999990 14 121 0.0026673520
##
## [1] "PrS_hyp_EPAS1_PTC_up"
## $reactome
## category over_represented_pvalue
## 225 cytosolic trna aminoacylation 1.17005e-05
## 632 metallothioneins bind metals 2.79189e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 225 0.9999988 9 24 0.01551486
## 632 0.9999992 5 8 0.01851023
##
## $go_bp
## category over_represented_pvalue
## 1417 intracellular zinc ion homeostasis 5.998904e-06
## 2599 organic acid transmembrane transport 6.465104e-06
## 98 amino acid transmembrane transport 6.881824e-06
## 4697 response to peptide hormone 2.074831e-05
## 1459 l alpha amino acid transmembrane transport 2.858616e-05
## 2774 polysaccharide metabolic process 3.893557e-05
## 456 cellular ketone metabolic process 6.228389e-05
## 1159 glucan metabolic process 6.996942e-05
## 924 energy reserve metabolic process 7.662500e-05
## 535 cellular response to peptide hormone stimulus 9.628083e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1417 0.9999993 10 30 0.01219689
## 2599 0.9999981 24 144 0.01219689
## 98 0.9999984 18 91 0.01219689
## 4697 0.9999904 46 389 0.02757969
## 1459 0.9999939 14 66 0.03039853
## 2774 0.9999898 17 90 0.03450341
## 456 0.9999765 27 198 0.04526835
## 1159 0.9999837 14 69 0.04526835
## 924 0.9999808 15 77 0.04526835
## 535 0.9999575 35 283 0.04948143
##
## [1] "PrS_hyp_EPAS1_PTC_down"
## $reactome
## category over_represented_pvalue
## 184 collagen chain trimerization 2.117636e-07
## 185 collagen degradation 8.060941e-06
## 183 collagen biosynthesis and modifying enzymes 1.917716e-05
## 253 degradation of the extracellular matrix 9.615816e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 184 1.0000000 11 42 0.0002807985
## 185 0.9999988 11 60 0.0053444036
## 183 0.9999969 11 65 0.0084763042
## 253 0.9999746 15 134 0.0318764295
##
## $go_bp
## category
## 322 canonical wnt signaling pathway
## 3732 regulation of canonical wnt signaling pathway
## 214 axon guidance
## 403 cell cell signaling by wnt
## 2166 negative regulation of locomotion
## 4175 regulation of nervous system development
## 4538 regulation of wnt signaling pathway
## 1982 negative regulation of canonical wnt signaling pathway
## 2404 negative regulation of wnt signaling pathway
## 1681 mesenchymal cell migration
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 322 5.542322e-08 1.0000000 31 295
## 3732 1.020704e-07 1.0000000 27 243
## 214 1.062720e-07 1.0000000 26 222
## 403 4.939242e-07 0.9999998 37 434
## 2166 7.025101e-07 0.9999998 30 315
## 4175 1.643157e-06 0.9999994 37 437
## 4538 1.829685e-06 0.9999994 29 317
## 1982 2.543725e-06 0.9999995 17 129
## 2404 2.968834e-06 0.9999993 19 161
## 1681 4.917748e-06 0.9999993 11 60
## FDR
## 322 0.0001883494
## 3732 0.0001883494
## 214 0.0001883494
## 403 0.0006565488
## 2166 0.0007470492
## 4175 0.0013897761
## 4538 0.0013897761
## 1982 0.0016906235
## 2404 0.0017539214
## 1681 0.0026147665
##
## [1] "ExM_nor_ISL1_CE_up"
## $reactome
## category over_represented_pvalue
## 746 olfactory signaling pathway 1.19631e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 746 0.9999979 12 89 0.01586306
##
## $go_bp
## category over_represented_pvalue
## 713 defense response to bacterium 7.160612e-08
## 39 acute inflammatory response 7.647093e-07
## 427 cell killing 6.358243e-06
## 1824 mononuclear cell migration 1.254278e-05
## 477 cellular response to biotic stimulus 2.129277e-05
## 2590 organ or tissue specific immune response 2.977281e-05
## 4679 response to molecule of bacterial origin 3.365707e-05
## 1502 leukocyte migration 3.681582e-05
## 242 bile acid and bile salt transport 4.787034e-05
## 3882 regulation of endocytosis 5.033140e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 713 1.0000000 22 209 0.0003807297
## 39 0.9999999 13 88 0.0020329797
## 427 0.9999986 16 156 0.0112689261
## 1824 0.9999971 16 165 0.0166724907
## 477 0.9999942 18 211 0.0226427321
## 2590 0.9999980 6 23 0.0244687119
## 4679 0.9999891 22 303 0.0244687119
## 1502 0.9999876 23 327 0.0244687119
## 242 0.9999964 6 25 0.0267612058
## 3882 0.9999842 20 267 0.0267612058
##
## [1] "ExM_nor_ISL1_CE_down"
## $reactome
## category over_represented_pvalue
## 346 extracellular matrix organization 1.384967e-07
## 253 degradation of the extracellular matrix 6.390523e-05
## 950 response to elevated platelet cytosolic ca2 1.022845e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 346 1.0000000 21 285 0.0001836466
## 253 0.9999877 11 134 0.0423691677
## 950 0.9999812 10 123 0.0452097438
##
## $go_bp
## category over_represented_pvalue
## 4552 renal system development 2.385023e-09
## 876 embryonic skeletal system development 8.918537e-09
## 165 appendage morphogenesis 2.262997e-08
## 5000 striated muscle tissue development 2.689309e-08
## 367 cardiocyte differentiation 3.751209e-08
## 164 appendage development 9.020386e-08
## 335 cardiac cell development 1.004327e-07
## 2166 negative regulation of locomotion 1.305182e-07
## 869 embryonic organ development 1.567302e-07
## 4850 sensory system development 1.791237e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 4552 1 26 314 1.268117e-05
## 876 1 15 115 2.370993e-05
## 165 1 16 141 3.574764e-05
## 5000 1 21 241 3.574764e-05
## 367 1 16 143 3.989035e-05
## 164 1 17 176 7.628578e-05
## 335 1 12 81 7.628578e-05
## 2166 1 23 315 8.674568e-05
## 869 1 27 424 9.259271e-05
## 4850 1 25 366 9.524008e-05
##
## [1] "ExM_nor_ISL1_KO_up"
## $reactome
## category over_represented_pvalue
## 746 olfactory signaling pathway 1.080823e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 746 1 14 89 1.433171e-05
##
## $go_bp
## category over_represented_pvalue
## 4847 sensory perception of smell 2.780553e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 4847 1 13 102 0.00147842
##
## [1] "ExM_nor_ISL1_KO_down"
## $reactome
## category over_represented_pvalue
## 346 extracellular matrix organization 3.418095e-07
## 253 degradation of the extracellular matrix 8.502496e-06
## 307 ecm proteoglycans 8.988685e-05
## 956 reversible hydration of carbon dioxide 1.282475e-04
## 185 collagen degradation 1.312697e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 346 0.9999999 20 285 0.0004532394
## 253 0.9999986 12 134 0.0056371552
## 307 0.9999876 8 75 0.0348127142
## 956 0.9999980 3 7 0.0348127142
## 185 0.9999840 7 60 0.0348127142
##
## $go_bp
## category over_represented_pvalue
## 165 appendage morphogenesis 1.587103e-09
## 876 embryonic skeletal system development 4.621993e-09
## 869 embryonic organ development 1.528846e-08
## 371 cartilage development 2.148341e-08
## 659 connective tissue development 4.292037e-08
## 164 appendage development 4.543318e-08
## 335 cardiac cell development 5.801474e-08
## 4850 sensory system development 6.577880e-08
## 4552 renal system development 8.631775e-08
## 1022 external encapsulating structure organization 8.873752e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 165 1 17 141 8.438627e-06
## 876 1 15 115 1.228757e-05
## 869 1 28 424 2.709625e-05
## 371 1 18 188 2.855682e-05
## 659 1 21 263 4.026137e-05
## 164 1 17 176 4.026137e-05
## 335 1 12 81 4.371823e-05
## 4850 1 25 366 4.371823e-05
## 4552 1 23 314 4.718174e-05
## 1022 1 22 302 4.718174e-05
##
## [1] "ExM_nor_ISL1_PTC_up"
## $reactome
## category over_represented_pvalue
## 746 olfactory signaling pathway 3.342164e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 746 1 12 89 4.431709e-05
##
## $go_bp
## category
## 4847 sensory perception of smell
## 5199 tyrosine phosphorylation of stat protein
## 3634 receptor signaling pathway via stat
## 3350 positive regulation of tyrosine phosphorylation of stat protein
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 4847 8.376484e-07 0.9999999 11 102
## 5199 1.767983e-05 0.9999981 8 69
## 3634 2.896012e-05 0.9999949 11 145
## 3350 3.278102e-05 0.9999968 7 55
## FDR
## 4847 0.004453776
## 5199 0.043574177
## 3634 0.043574177
## 3350 0.043574177
##
## [1] "ExM_nor_ISL1_PTC_down"
## $reactome
## category
## 346 extracellular matrix organization
## 307 ecm proteoglycans
## 253 degradation of the extracellular matrix
## 950 response to elevated platelet cytosolic ca2
## 910 regulation of insulin like growth factor igf transport and uptake by insulin like growth factor binding proteins igfbps
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 346 2.630596e-08 1.0000000 19 285
## 307 1.386547e-05 0.9999985 8 75
## 253 2.575236e-05 0.9999960 10 134
## 950 6.134437e-05 0.9999906 9 123
## 910 1.513934e-04 0.9999772 8 112
## FDR
## 346 3.488171e-05
## 307 9.192807e-03
## 253 1.138254e-02
## 950 2.033566e-02
## 910 4.014954e-02
##
## $go_bp
## category over_represented_pvalue
## 165 appendage morphogenesis 2.243689e-10
## 164 appendage development 5.927931e-09
## 876 embryonic skeletal system development 1.096842e-08
## 4850 sensory system development 2.860701e-08
## 371 cartilage development 9.997279e-08
## 852 embryonic appendage morphogenesis 1.346438e-07
## 4552 renal system development 2.635309e-07
## 869 embryonic organ development 2.736724e-07
## 335 cardiac cell development 3.262088e-07
## 659 connective tissue development 3.366968e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 165 1.0000000 16 141 1.192969e-06
## 164 1.0000000 16 176 1.575940e-05
## 876 1.0000000 13 115 1.943970e-05
## 4850 1.0000000 22 366 3.802587e-05
## 371 1.0000000 15 188 1.063111e-04
## 852 1.0000000 12 117 1.193169e-04
## 4552 0.9999999 19 314 1.790217e-04
## 869 0.9999999 22 424 1.790217e-04
## 335 1.0000000 10 81 1.790217e-04
## 659 0.9999999 17 263 1.790217e-04## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8857532 473.1 15591512 832.7 NA 15591512 832.7
## Vcells 22997502 175.5 73154941 558.2 65536 91443676 697.7## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] data.table_1.14.8
## [12] dplyr_1.1.2
## [13] fgsea_1.24.0
## [14] goseq_1.50.0
## [15] geneLenDataBase_1.34.0
## [16] BiasedUrn_2.0.10
## [17] RColorBrewer_1.1-3
## [18] stringr_1.5.0
## [19] ggpubr_0.6.0
## [20] ggrepel_0.9.3
## [21] ggplot2_3.4.2
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.1-0 ggsignif_0.6.4
## [3] rjson_0.2.21 XVector_0.38.0
## [5] rstudioapi_0.14 bit64_4.0.5
## [7] fansi_1.0.4 xml2_1.3.4
## [9] codetools_0.2-19 splines_4.2.3
## [11] R.methodsS3_1.8.2 cachem_1.0.7
## [13] knitr_1.44 jsonlite_1.8.4
## [15] Rsamtools_2.14.0 broom_1.0.4
## [17] GO.db_3.16.0 dbplyr_2.3.2
## [19] png_0.1-8 R.oo_1.25.0
## [21] compiler_4.2.3 httr_1.4.6
## [23] backports_1.4.1 Matrix_1.6-4
## [25] fastmap_1.1.1 cli_3.6.1
## [27] htmltools_0.5.5 prettyunits_1.1.1
## [29] tools_4.2.3 gtable_0.3.3
## [31] glue_1.6.2 GenomeInfoDbData_1.2.9
## [33] rappdirs_0.3.3 fastmatch_1.1-3
## [35] Rcpp_1.0.10 carData_3.0-5
## [37] jquerylib_0.1.4 vctrs_0.6.2
## [39] Biostrings_2.66.0 nlme_3.1-162
## [41] rtracklayer_1.58.0 xfun_0.39
## [43] lifecycle_1.0.3 restfulr_0.0.15
## [45] rstatix_0.7.2 XML_3.99-0.14
## [47] zlibbioc_1.44.0 scales_1.2.1
## [49] hms_1.1.3 MatrixGenerics_1.10.0
## [51] parallel_4.2.3 SummarizedExperiment_1.28.0
## [53] yaml_2.3.7 curl_5.0.1
## [55] memoise_2.0.1 sass_0.4.5
## [57] biomaRt_2.54.1 stringi_1.7.12
## [59] RSQLite_2.3.1 BiocIO_1.8.0
## [61] filelock_1.0.2 BiocParallel_1.32.6
## [63] rlang_1.1.0 pkgconfig_2.0.3
## [65] matrixStats_1.0.0 bitops_1.0-7
## [67] evaluate_0.20 lattice_0.20-45
## [69] purrr_1.0.1 GenomicAlignments_1.34.1
## [71] cowplot_1.1.1 bit_4.0.5
## [73] tidyselect_1.2.0 magrittr_2.0.3
## [75] R6_2.5.1 generics_0.1.3
## [77] DelayedArray_0.24.0 DBI_1.1.3
## [79] pillar_1.9.0 withr_2.5.0
## [81] mgcv_1.8-42 KEGGREST_1.38.0
## [83] abind_1.4-5 RCurl_1.98-1.12
## [85] tibble_3.2.1 crayon_1.5.2
## [87] car_3.1-2 utf8_1.2.3
## [89] BiocFileCache_2.6.1 rmarkdown_2.21
## [91] progress_1.2.2 grid_4.2.3
## [93] blob_1.2.4 digest_0.6.31
## [95] tidyr_1.3.0 R.utils_2.12.2
## [97] munsell_0.5.0 bslib_0.4.2